6YUT

Structure of recombinant human beta-glucocerebrosidase in complex with N-acyl functionalised cyclophellitol aziridine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NT0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2911 M (NH3)2SO4, 0.17 M guanidine HCl, 0.03 M KCl, 0.1 M sodium acetate pH 4.6
Crystal Properties
Matthews coefficientSolvent content
3.2662.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.699α = 90
b = 285.525β = 90
c = 91.902γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2016-01-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.979490DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7647.63399.80.0980.0420.997106.3143462
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.761.7999.90.8450.370.8351.76.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2NT01.7647.633143436716099.70.1840.1830.208431.049
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
5.597-2.895-2.702
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.051
r_dihedral_angle_4_deg20.04
r_dihedral_angle_3_deg13.978
r_dihedral_angle_1_deg7.202
r_lrange_it6.016
r_lrange_other6.016
r_dihedral_angle_other_1_deg4.82
r_scangle_it4.192
r_scangle_other4.192
r_mcangle_it2.913
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.051
r_dihedral_angle_4_deg20.04
r_dihedral_angle_3_deg13.978
r_dihedral_angle_1_deg7.202
r_lrange_it6.016
r_lrange_other6.016
r_dihedral_angle_other_1_deg4.82
r_scangle_it4.192
r_scangle_other4.192
r_mcangle_it2.913
r_mcangle_other2.913
r_scbond_it2.649
r_scbond_other2.648
r_mcbond_it1.931
r_mcbond_other1.931
r_angle_refined_deg1.447
r_angle_other_deg1.267
r_nbd_refined0.202
r_nbd_other0.185
r_symmetry_nbd_other0.182
r_symmetry_nbd_refined0.179
r_symmetry_xyhbond_nbd_refined0.169
r_nbtor_refined0.165
r_xyhbond_nbd_refined0.162
r_symmetry_nbtor_other0.079
r_chiral_restr0.071
r_symmetry_xyhbond_nbd_other0.055
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7808
Nucleic Acid Atoms
Solvent Atoms735
Heterogen Atoms314

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing